def write_MC_poscar(atoms_in, Ef, istep=0):
atoms = copy.deepcopy(atoms_in)
if istep > 0.5:
pos_name = 'POSCAR_step_%d_Ef_%+.3f' % (istep, Ef)
else:
pos_name = 'POSCAR_Ef_%+.3f' % (Ef)
vf.my_write_vasp(atoms, filename=pos_name, vasp5=True)
def vasp_create_fcc_100(a, ncell, bp=0):
print('==> create fcc 100 plane: ')
print(a, ncell, bp)
latt = np.array([
[1.0, 0, 0],
[0, 1.0, 0],
[0, 0, 1.0],
]) * a
motif = np.array([
[0, 0, 0],
[0.5, 0.5, 0],
[0.5, 0, 0.5],
[0, 0.5, 0.5],
])
atoms = vf.create_supercell(latt, motif, ncell)
atoms.pos_a0 = a
if bp == 33:
atoms.positions = atoms.positions + np.array([0, 0, 0.1]) *a
atoms.wrap()
vf.my_write_vasp(atoms, filename='POSCAR', vasp5=True)
def vasp_create_hcp_pyr1(a, ca, ncell, bp=33):
print('==> create hcp basal pyr1: ')
print(a, ca, ncell, bp)
latt = np.array([
[1.0, 0, 0],
[0.5, np.sqrt(3) / 2, 0],
[-1.0, 0, ca],
]) * a
motif = np.array([
[0, 0, 0],
[1 / 6, 2 / 3, 1 / 2],
])
ncell2 = ncell.copy()
for i in np.arange(3):
ncell2[i] = ncell[np.mod(i + 2, 3)]
atoms = vf.create_supercell(latt, motif, ncell2)
atoms = vf.make_SFP_xy(atoms, i1=1)
atoms = vf.make_a3_ortho(atoms)
if bp == 33:
print('==> create pry1-W')
atoms.positions = atoms.positions + np.array([0, 0, 0.1]) * a
atoms.wrap()
elif bp == -33:
print('==> create pry1-N')
atoms.positions = atoms.positions + np.array([0, 0, -0.05]) * a
atoms.wrap()
atoms.pos_a0 = a
vf.my_write_vasp(atoms, filename='POSCAR', vasp5=True)
def vasp_create_fcc_111_ortho(a, ncell, bp=0):
print('==> create fcc 111 plane (ortho): ')
print(a, ncell, bp)
latt = np.array([
[1, 0, 0],
[0, np.sqrt(3), 0],
[0, 0, np.sqrt(6)],
]) * a/np.sqrt(2)
motif = np.array([
[ 0, 0, 0],
[1/2, 1/2, 0],
[ 0, 4/6, 1/3],
[1/2, 1/6, 1/3],
[ 0, 2/6, 2/3],
[1/2, 5/6, 2/3],
])
atoms = vf.create_supercell(latt, motif, ncell)
atoms.pos_a0 = a
if bp == 33:
atoms.positions = atoms.positions + np.array([0, 0, 0.1]) *a
atoms.wrap()
vf.my_write_vasp(atoms, filename='POSCAR', vasp5=True)
def vasp_create_hcp_prism1(a, ca, ncell, bp=33):
print('==> create hcp prism plane: ')
print(a, ca, ncell, bp)
ncell2 = ncell.copy()
for i in np.arange(3):
ncell2[i] = ncell[np.mod(i + 2, 3)]
vasp_create_hcp_basal(a, ca, ncell2, bp=0)
atoms = vf.my_read_vasp('POSCAR')
atoms = vf.make_SFP_xy(atoms, i1=1)
atoms = vf.make_a3_ortho(atoms)
if bp == 33:
print('==> create prism1-W')
atoms.positions = atoms.positions + np.array([0, 0, 0.1]) * a
atoms.wrap()
elif bp == -33:
print('==> create prism1-N')
atoms.positions = atoms.positions + np.array([0, 0, -0.1]) * a
atoms.wrap()
atoms.pos_a0 = a
vf.my_write_vasp(atoms, filename='POSCAR', vasp5=True)
def vasp_create_hcp_basal_ortho(a, ca, ncell, bp=33):
print('==> create hcp basal_ortho plane: ')
print(a, ca, ncell, bp)
latt = np.array([
[1.0, 0, 0],
[0, np.sqrt(3), 0],
[0, 0, ca],
]) * a
motif = np.array([
[0.0, 0, 0],
[1 / 2, 1 / 2, 0],
[0, 2 / 6, 1 / 2],
[1 / 2, 5 / 6, 1 / 2],
])
atoms = vf.create_supercell(latt, motif, ncell)
if bp == 33:
atoms.positions = atoms.positions + np.array([0, 0, 0.1]) * a
atoms.wrap()
atoms.pos_a0 = a
vf.my_write_vasp(atoms, filename='POSCAR', vasp5=True)
def vasp_create_bcc_123(a, ncell, bp=0):
print('==> create bcc 12-3 plane: ')
print(a, ncell, bp)
latt = np.array([
[1.0, 0, 0],
[1 / 2, 1 / 2, 1 / 2],
[5 / 2, -1 / 2, 1 / 2],
]) * a
motif = np.array([
[0, 0, 0],
])
ncell2 = ncell.copy()
for i in np.arange(3):
ncell2[i] = ncell[np.mod(i + 2, 3)]
atoms = vf.create_supercell(latt, motif, ncell2)
atoms = vf.make_SFP_xy(atoms, i1=1)
atoms = vf.make_a3_ortho(atoms)
if bp == 33:
atoms.positions = atoms.positions + np.array([0, 0, 0.1]) * a
atoms.wrap()
atoms.pos_a0 = a
vf.my_write_vasp(atoms, filename='POSCAR', vasp5=True)
def calc_pairs_per_shell(atoms_in, shellmax=4, write_dp=True):
atoms = copy.deepcopy(atoms_in)
print('==> shellmax: ', shellmax)
vf.my_rm('y_post_dp_shell.txt')
natoms = atoms.get_positions().shape[0]
V0 = atoms.get_volume() / natoms
a0 = (V0 * 4)**(1 / 3)
cn = atoms.get_cn()
print('==> a0: ', a0, '; cn: ', cn)
cc_scale = calc_cc_scale(cn)
vf.my_write_vasp(atoms, filename='CONTCAR_for_ovito', vasp5=True)
struc = calc_ovito_cna(atoms)
rcrys, ncrys = crystal_shell(struc)
cutoff = a0 * rcrys[shellmax - 1] + 1e-5
data_rdf = calc_ovito_rdf(atoms, cutoff)
r, n = post_rdf(data_rdf, V0, cc_scale)
while np.abs(n.sum() - ncrys[0:shellmax].sum()) > 1e-10:
if n.sum() > ncrys[0:shellmax].sum():
sys.exit('==> ABORT. impossible cutoff. ')
cutoff = cutoff + 0.1
data_rdf = calc_ovito_rdf(atoms, cutoff)
r, n = post_rdf(data_rdf, V0, cc_scale)
dn_shell, WC_SRO = calc_n_shell(ncrys, shellmax, r, n, cc_scale)
rmid = calc_rmid(cn)
dn_shell_r = read_reduced_dn_shell(dn_shell, rmid)
WC_SRO_r = read_reduced_dn_shell(WC_SRO, rmid)
dpw = np.prod(dn_shell_r.shape) # dp width
dp_shell = dn_shell_r.reshape(dpw) / 2
WC_SRO_r2 = WC_SRO_r.reshape(dpw)
if write_dp == True:
np.savetxt("y_post_dp_shell.txt", dp_shell)
np.savetxt("y_post_WC_SRO_shell.txt", WC_SRO_r2)
return dp_shell
def vasp_create_fcc_111_min(a, ncell, bp=0):
print('==> create fcc 111 plane min: ')
print(a, ncell, bp)
latt = np.array([
[1, 0, 0],
[-0.5, np.sqrt(3)/2, 0],
[ 0.5, np.sqrt(3)/6, np.sqrt(6)/3],
]) * a/np.sqrt(2)
motif = np.array([
[0, 0, 0],
])
atoms = vf.create_supercell(latt, motif, ncell)
atoms.pos_a0 = a
if bp == 33:
atoms.positions = atoms.positions + np.array([0, 0, 0.1]) *a
atoms.wrap()
vf.my_write_vasp(atoms, filename='POSCAR', vasp5=True)
def shift_to_poscar_layer(nmiss):
atoms = vf.my_read_vasp(filename='CONTCAR')
z = atoms.get_positions()[:, -1]
z.sort()
natoms = len(z)
latt33 = atoms.get_cell()[2, 2]
temp1 = latt33 - z[int(-1 * nmiss)]
temp2 = z[int(-1 * nmiss)] - z[int(-1 * nmiss - 1)]
zshift = temp1 + 0.5 * temp2
pos = atoms.get_positions()
pos[:, 2] = pos[:, 2] + zshift
atoms.set_positions(pos)
atoms.wrap()
vf.my_write_vasp(atoms, filename='POSCAR_layer', vasp5=True)
# check
atoms2 = vf.my_read_vasp('POSCAR_layer')
atoms3 = vf.my_read_vasp('CONTCAR')
latt = atoms2.get_cell()[:]
vf.confirm_0(latt - atoms3.get_cell()[:])
dpos = atoms2.get_positions() - atoms3.get_positions()
dposD = dpos @ np.linalg.inv(latt)
dposD = dposD - np.around(dposD)
dpos = dposD @ latt
for i in np.arange(3):
dpos[:, i] = dpos[:, i] - dpos[:, i].mean()
vf.confirm_0(dpos)
def create_random_alloys(atoms_in,
cn,
nsamples=1,
filename='POSCAR',
id1=1,
vasp5=False):
atoms = copy.deepcopy(atoms_in)
natoms = atoms.get_positions().shape[0]
# calc natoms_elem
cn = cn / cn.sum()
natoms_elem = np.around(cn * natoms)
if natoms_elem.min() < 0.1:
sys.exit('==> ABORT. natoms is too small. ')
max_elem = np.argmax(natoms_elem)
temp = natoms_elem.sum() - natoms_elem[max_elem]
natoms_elem[max_elem] = natoms - temp
print(natoms_elem)
# new symbols
symb = np.array([])
for i in np.arange(natoms_elem.shape[0]):
for j in np.arange(natoms_elem[i]):
symb = np.append(symb, i + 1)
atoms.set_chemical_symbols(symb)
# randomize pos
for i in np.arange(nsamples):
temp = np.hstack([ atoms.positions, \
np.random.random_sample([natoms, 1]) ])
ind = np.argsort(temp[:, -1])
atoms.set_positions(temp[ind, 0:3], apply_constraint=False)
filename2 = '%s_%03d' % (filename, i + id1)
vf.my_write_vasp(atoms, filename2, vasp5=vasp5)